1EMJ: Uracil-DNA glycosylase

Uracil-DNA glycosylase bound to DNA containing a 4'-thio-2'DEOXYURIDINE analog product. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 May 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,353
Mol. weight: 31.35 kDa
Ligands: URA
Released: 16 May 2000

Explore 1EMJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1EMJ contains 15 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	87-93	7
α-helix	94-96	3
α-helix	100-115	16
β-strand	118-119	2	1
α-helix	122-124	3
α-helix	127-129	3
α-helix	134-136	3
β-strand	139-143	5	2
α-helix	165-167	3
α-helix	168-180	13
α-helix	193-196	4
β-strand	200-204	5	2
β-strand	209-210	2	1
α-helix	222-236	15
β-strand	241-245	5	2
α-helix	247-250	4
α-helix	251-255	5
β-strand	262-266	5	2
α-helix	274-276	3
α-helix	283-293	11
α-helix	296-299	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(tpgptp(asu)paptpcptp*t)-3')	B	DNA	9
DNA (5'-d(apapapgpaptpapapcpa)-3')	C	DNA	10
Uracil-DNA glycosylase	A	protein	223	Homo sapiens	P13051 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1EMJ_1 DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3') (chains B)
TGTNATCTT

Sequence of entity 2 (C), FASTA

>1EMJ_2 DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3') (chains C)
AAAGATAACA

Sequence of entity 3 (A), FASTA

>1EMJ_3 URACIL-DNA GLYCOSYLASE (chains A)
MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVI
LGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVL
LLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRH
HVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL

Ligands and cofactors

ID	Name	Formula	Copies
URA	Uracil	C4 H4 N2 O2	1

Primary citation

Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Parikh, S.S., Walcher, G., Jones, G.D. et al. Proc Natl Acad Sci U S A (2000) 97:5083-5088. DOI 10.1073/pnas.97.10.5083 · PubMed

Other PDB entries of the same protein (UniProt P13051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FCI 1.27 Å, Complex of UNG2 and a fragment-based designed inhibitor
2HXM 1.3 Å, Complex of UNG2 and a small Molecule synthetic Inhibitor
3TKB 1.5 Å, crystal structure of human uracil-DNA glycosylase D183G/K302R mutant
1AKZ 1.57 Å, Human uracil-DNA glycosylase
3FCK 1.64 Å, Complex of UNG2 and a fragment-based design inhibitor
3FCL 1.7 Å, Complex of UNG2 and a fragment-based designed inhibitor
9LNQ 1.74 Å, The hUNG bound to DNA product embedding 4primer-OCH3-dU
9LNP 1.76 Å, the hUNG bound to DNA product embedding uridine ribonucleotide
1EMH 1.8 Å, Crystal structure of human uracil-DNA glycosylase bound to uncleaved…
6VBA 1.8 Å, Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA)
3FCF 1.84 Å, Complex of UNG2 and a fragment-based designed inhibitor
1Q3F 1.9 Å, Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Browse structure collections

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